Literature DB >> 31119604

Z-DNA in the genome: from structure to disease.

Subramaniyam Ravichandran1, Vinod Kumar Subramani1, Kyeong Kyu Kim2,3.   

Abstract

The scope of studies investigating the architecture of genomic DNA has progressed steadily since the elucidation of the structure of B-DNA. In recent years, several non-canonical DNA structures including Z-DNA, G-quadruplexes, H-DNA, cruciform DNA, and i-motifs have been reported to form in genomic DNA and are closely related to the evolution and development of disease. The ability of these structures to form in genomic DNA indicates that they might have important cellular roles and are therefore retained during evolution. Understanding the impact of the formation of these secondary structures on cellular processes can enable identification of new targets for therapeutics. In this review, we report the state of understanding of Z-DNA structure and formation and their implication in disease. Finally, we state our perspective on the potential of Z-DNA as a therapeutic target.

Keywords:  Disease; Therapeutic target; Transcription; Z-DNA; Z-DNA-binding protein

Year:  2019        PMID: 31119604      PMCID: PMC6557933          DOI: 10.1007/s12551-019-00534-1

Source DB:  PubMed          Journal:  Biophys Rev        ISSN: 1867-2450


  36 in total

1.  Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases.

Authors:  Sung Chul Ha; Ky Lowenhaupt; Alexander Rich; Yang-Gyun Kim; Kyeong Kyu Kim
Journal:  Nature       Date:  2005-10-20       Impact factor: 49.962

Review 2.  Z-DNA, an active element in the genome.

Authors:  Guliang Wang; Karen M Vasquez
Journal:  Front Biosci       Date:  2007-05-01

3.  Incorporation of CC steps into Z-DNA: interplay between B-Z junction and Z-DNA helical formation.

Authors:  Jameson R Bothe; Ky Lowenhaupt; Hashim M Al-Hashimi
Journal:  Biochemistry       Date:  2012-08-17       Impact factor: 3.162

4.  Chemical-induced formation of BZ-junction with base extrusion.

Authors:  Vinod Kumar Subramani; Subramaniyam Ravichandran; Varun Bansal; Kyeong Kyu Kim
Journal:  Biochem Biophys Res Commun       Date:  2018-12-14       Impact factor: 3.575

5.  Transcriptional block caused by a negative supercoiling induced structural change in an alternating CG sequence.

Authors:  L J Peck; J C Wang
Journal:  Cell       Date:  1985-01       Impact factor: 41.582

Review 6.  Left-handed Z-DNA and genetic recombination.

Authors:  J A Blaho; R D Wells
Journal:  Prog Nucleic Acid Res Mol Biol       Date:  1989

7.  8-Methylguanosine: a powerful Z-DNA stabilizer.

Authors:  Yan Xu; Reiko Ikeda; Hiroshi Sugiyama
Journal:  J Am Chem Soc       Date:  2003-11-05       Impact factor: 15.419

8.  A computer aided thermodynamic approach for predicting the formation of Z-DNA in naturally occurring sequences.

Authors:  P S Ho; M J Ellison; G J Quigley; A Rich
Journal:  EMBO J       Date:  1986-10       Impact factor: 11.598

9.  Distinct Z-DNA binding mode of a PKR-like protein kinase containing a Z-DNA binding domain (PKZ).

Authors:  Doyoun Kim; Jeonghwan Hur; Kwangsoo Park; Sangsu Bae; Donghyuk Shin; Sung Chul Ha; Hye-Yeon Hwang; Sungchul Hohng; Joon-Hwa Lee; Sangho Lee; Yang-Gyun Kim; Kyeong Kyu Kim
Journal:  Nucleic Acids Res       Date:  2014-03-20       Impact factor: 16.971

10.  Sequence preference and structural heterogeneity of BZ junctions.

Authors:  Doyoun Kim; Jeonghwan Hur; Ji Hoon Han; Sung Chul Ha; Donghyuk Shin; Sangho Lee; Soyoung Park; Hiroshi Sugiyama; Kyeong Kyu Kim
Journal:  Nucleic Acids Res       Date:  2018-11-02       Impact factor: 16.971

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  12 in total

Review 1.  Energetics of twisted DNA topologies.

Authors:  Wenxuan Xu; David Dunlap; Laura Finzi
Journal:  Biophys J       Date:  2021-05-08       Impact factor: 3.699

2.  MD-TSPC4: Computational Method for Predicting the Thermal Stability of I-Motif.

Authors:  Amen Shamim; Maria Razzaq; Kyeong Kyu Kim
Journal:  Int J Mol Sci       Date:  2020-12-23       Impact factor: 5.923

Review 3.  Beyond the double helix: DNA structural diversity and the PDB.

Authors:  Stephen Neidle
Journal:  J Biol Chem       Date:  2021-03-17       Impact factor: 5.157

Review 4.  The Anti-DNA Antibodies: Their Specificities for Unique DNA Structures and Their Unresolved Clinical Impact-A System Criticism and a Hypothesis.

Authors:  Ole Petter Rekvig
Journal:  Front Immunol       Date:  2022-01-11       Impact factor: 7.561

5.  Dual targeting of higher-order DNA structures by azacryptands induces DNA junction-mediated DNA damage in cancer cells.

Authors:  Joanna Zell; Katerina Duskova; Leïla Chouh; Madeleine Bossaert; Nicolas Chéron; Anton Granzhan; Sébastien Britton; David Monchaud
Journal:  Nucleic Acids Res       Date:  2021-10-11       Impact factor: 16.971

Review 6.  The Dynamic Regulation of G-Quadruplex DNA Structures by Cytosine Methylation.

Authors:  Aaron John Stevens; Lucy de Jong; Martin Alexander Kennedy
Journal:  Int J Mol Sci       Date:  2022-02-22       Impact factor: 5.923

Review 7.  DNA folds threaten genetic stability and can be leveraged for chemotherapy.

Authors:  Joanna Zell; Francesco Rota Sperti; Sébastien Britton; David Monchaud
Journal:  RSC Chem Biol       Date:  2020-09-30

8.  Deep learning approach for predicting functional Z-DNA regions using omics data.

Authors:  Nazar Beknazarov; Seungmin Jin; Maria Poptsova
Journal:  Sci Rep       Date:  2020-11-05       Impact factor: 4.379

9.  Dual conformational recognition by Z-DNA binding protein is important for the B-Z transition process.

Authors:  Chaehee Park; Xu Zheng; Chan Yang Park; Jeesoo Kim; Seul Ki Lee; Hyuk Won; Jinhyuk Choi; Yang-Gyun Kim; Hee-Jung Choi
Journal:  Nucleic Acids Res       Date:  2020-12-16       Impact factor: 16.971

10.  G-quadruplex DNA inhibits unwinding activity but promotes liquid-liquid phase separation by the DEAD-box helicase Ded1p.

Authors:  Jun Gao; Zhaofeng Gao; Andrea A Putnam; Alicia K Byrd; Sarah L Venus; John C Marecki; Andrea D Edwards; Haley M Lowe; Eckhard Jankowsky; Kevin D Raney
Journal:  Chem Commun (Camb)       Date:  2021-07-27       Impact factor: 6.222

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